Research workbench
Full-length human mitochondrial HSP90 (TRAP1) SPYCATCHER/SPYTAG-sdhb heterodimer in the presence of AMP-pnp
Analyse Full-length human mitochondrial HSP90 (TRAP1) SPYCATCHER/SPYTAG-sdhb… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KLV
- Type
- protein
- Length
- 1,226 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heat shock protein 75 kda, mitochondrial, spycatcher; Heat shock protein 75 kda…
- EC
- 1.3.5.1
- UniProt
- Q12931
- Ligands
- ANP, MG, K
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heat shock protein 75 kda, mitochondrial, spycatcher | protein | 612 | 39% helix, 18% strand | Q12931 |
| B | Heat shock protein 75 kda, mitochondrial, spytag, succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial (chimera) (EC 1.3.5.1) | protein | 614 | 40% helix, 18% strand | Q12931 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.80 | 0.84 | 54 | empty |
| 2 | 483 | 0.80 | 0.87 | 63 | ANP, MG |
| 3 | 482 | 0.79 | 0.87 | 62 | ANP, MG, K |
| 4 | 54 | 0.71 | 0.97 | 16 | empty |
| 5 | 186 | 0.69 | 0.87 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 5441 Ų buried · 53 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7KLV · Full-length human mitochondrial Hsp90 (TRAP1) SpyCatcher/SpyTag-SdhB heterodimer in the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q12931 · AlphaFold monomer V2.0 prediction for heat shock protein 75 kda, mitochondrial (Q12931) · a predicted model of the same protein · chain B against A, TM-score 0.96
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q12931
- Elsewhere: RCSB PDB 7KLV · PDBe 7KLV · UniProt Q12931
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